Aftermath Chapter 3
by DJH1950
Summary: Chapter 2 ended at a dinner party, this is what happens next.
1. Chapter 1

**_Aftermath's Grand Adventure ended just as a dinner party was starting. Here's the next installment. Thanks to all who've read the series. As always, reviews and critiques are welcomed. I own none of these characters._**

Harold Finch pushed his chair back and smiled.

"Ms. Shaw, Ms. Groves, that was magnificent. If I didn't know better, I'd think we were at a four star restaurant. Spinach salad, beef tenderloin to die for, twice baked potatoes- I haven't eaten like that since Grace and I were in Europe. No offense to the hospital's food, Dr. Tillman."

Dr. Megan Tillman turned her head at her name. She had been sneaking glances at Elizabeth all evening and, after her third Scotch, the glances were lasting longer and longer. She was feeling a pleasant buzz and, had anyone commented on it, would have blamed the liquor for the flush that positively glowed from her cheeks.

 _Not from her proximity to the hot and intriguing lady sitting next to her._

Elizabeth's knee brushed up against the doctor's leg as she turned to Shaw. Reaching across Dr. Tillman to pat Shaw's hand, she _accidentally_ grazed the front of Dr. Tillman's blouse and smiled at her.

"Shaw, Root you guys have really come a long way. This was amazing and your house is beautiful."

Shaw smirked, not fooled by Elizabeth's gesture and opened her mouth to make a comment almost certainly laced with innuendo. Root, sensing it and the potential danger, chimed in before Shaw could reply.

"Sameen and I fell in love with this place when we first laid eyes on it. Actually, she fell in love with it first, but I agreed instantly when she showed it to me. It's like both of them knew this was the perfect place for us."

As Shaw looked over at Root, she saw the message in her eyes. _Leave Elizabeth and Dr. Tillman alone._ Shaw smirked, shrugged and nodded at Root. As Root rose to clear the table, she asked if anyone wanted coffee or to freshen their drink. Shaw also rose to her feet.

"Let me help you babe. In fact, why don't you take our guests into the living room and let me handle the dishes and drinks?"

Root smiled at her. "I'll help you with the first load, then bring the drinks back."

Shaw nodded and began to gather the dishes. Harold and John rose from the table and each grabbed a handful of dishes. Harold looked over at Elizabeth and Dr. Tillman.

"John and I rode out in a separate car and I think we're both ready to head back to the hospital. This was wonderful, I hope we can do it again when Grace returns from Europe."

Root smiled, "Of course, Harry, you all have a standing invitation here. In fact, if you want, you can stay the night any time you want or possibly need to due to excess alcohol consumption." She glanced at Dr. Tillman and winked. John shook his head and coughed to cover a laugh- both at Root's reference to Dr. Tillman's state and at her wink, which was pure comedy to everyone except Sameen who, for some unexplainable reason, got a lump in her throat every time Root winked at her.

Fortunately, she had already headed for the kitchen. As John and Harold headed for the basement and the garage, Root said, "Just a minute, I'll see you out."

John went into the kitchen, walked over and hugged Shaw, then Root. "We're adults, sweetheart, I'll even put the garage door down when we leave." Returning to the dining room he smiled at Elizabeth and the doctor. "Goodnight ladies," John added to Elizabeth and Dr. Tillman.

Elizabeth smiled and nodded. Dr. Tillman giggled and glanced at Elizabeth again, cheeks flaming.

"I hope so."

The two men smiled and headed for the basement.

Root returned to the dining room with the Scotch in one hand and the wine in the other.

"Elizabeth, there's more Heineken in the fridge in the basement. Maybe we should head down there."

As they headed to the stairway, Root called over her shoulder.

"Sam, we'll be at the bar."

"Be there in a minute."

….

Two hours later, Root yawned and looked at her friends.

"This has been fun, but I think I need to go to bed. Sam, I think our friends should stay the night- don't you?"

"I'm not letting them drive after all this." Shaw indicated the empty Scotch bottle and several empty beer bottles. "I'll get them set up and be up in a few minutes."

"Don't take too long, Sameen."

The two shared a look that could have ignited a four-alarm fire in an oil refinery. Root's neck tinged slightly pink as she headed up the stairs. Elizabeth glanced at Shaw, noticing the flush that was creeping up her face, and decided to ignore it.

She had other things on her mind.

Shaw walked over to the "guest suite" which consisted of three doors beyond a small sitting area.

"The middle door is the bathroom, each bedroom has clean sheets and the beds are already made up. We have bathrobes in each closet, but we don't have any nightclothes. Sorry, but we're not Bed, Bath and Beyond."

She rolled her eyes. Elizabeth, smirking, leered at Dr. Tillman.

"It's OK Shaw, I never wear _anything_ to bed."

Dr. Tillman's skin (amazingly) blushed even more. She glanced at Elizabeth, then at Shaw, then her eyes glazed over momentarily. She tried to speak, then cleared her throat and began again.

"I'll be f… fine."

Shaw finished cleaning off the bar and walked around to where their two guests were still seated. Wrapping an arm around Elizabeth, she briefly brushed her lips on her cheek.

"Tread softly tiger," she whispered in Elizabeth's ear. Turning to Dr. Tillman she smiled and hugged her newfound friend.

"Goodnight, doctor, I can't tell you what a godsend you are to us all."

"Goodnight, Ms. Shaw, I… I…" Whatever the doctor wanted to say was apparently lost in the alcohol induced fog several Scotches over four hours had created. She appeared lucid, but complicated thoughts weren't going to be making it out of her mouth until morning. She simply smiled and returned the hug.

As Shaw headed for the stairs, she couldn't help a thought from flashing through her mind.

 _Oh to be a fly on the wall._

 _…_ _._

As Shaw disappeared up the stairs, Elizabeth looked over at Dr. Tillman. Both ladies were still seated next to each other at the bar, drinks in front of them. As the doctor's eyes came up to meet Elizabeth's, she saw something and, finding both her voice and her courage, stared into her companion's eyes.

"So…. where is this going, Elizabeth?"

Ellie locked eyes with Tillman, but didn't speak. She didn't want to scare the doctor, but she also knew she wasn't the one who had to make a decision. After a moment (an hour? a day? an eternity?), the doctor smiled and raised her eyebrows.

"What's the matter? Cat got your…"

She never finished the sentence as Elizabeth's lips converged on hers- softly at first, then with a fury that surprised them both. Minutes later, as they both came up for air, Elizabeth drew back, and with a smirk, said,

"Your place or mine, doctor?"

Dr. Tillman, feeling emboldened, stood from her chair and took Elizabeth's hand.

"I really don't care, but if we're going in there, you better start calling me Megan."

Elizabeth stood and wrapped her free hand around Megan's neck. As she drew their heads together, she spoke softly, barely above a whisper.

"Then, call me Beth."


	2. Chapter 2

Shaw's eyes opened as she slowly came back to consciousness. The evening's activities came flooding back and she became aware of the familiar ache that resulted from another night of fireworks. Smiling, she glanced at the time.

 _4:15- I wonder what woke me up._

As Shaw turned over she became aware of something disturbing the bed. Rising up on one elbow, she saw Root shaking, almost convulsing in her sleep. She reached for her love, gently shaking her shoulder.

The room was faintly bathed in moonlight- as a result, Shaw could see Root's eyes squeezed tightly shut as she continued to shake uncontrollably. Then, suddenly, her eyes opened. She stared unseeing at the ceiling as the shaking continued.

Alarmed, Shaw grabbed Root with both hands and shook her harder.

"Root, are you OK? Root, hey…. ROOT!"

Root's eyes blinked once, twice, then cleared as the shaking subsided. Shaw, concerned, leaned over and brushed the hair from her face.

"Hey babe, you all right?"

"Sameen…. I…. I think I was having a nightmare."

"Well, now I'm wide awake- I need a drink of water." Shaw climbed out of bed and headed for the kitchen. Root sat up and rubbed her eyes.

"I'll be right there, after I go to the bathroom."

"Relax, I'll bring us both a bottle."

"Thanks, Sam."

Shaw headed into the kitchen and went to the fridge for a couple bottles of water. _Only three left, I could go down and get….._ her thoughts trailed off as she remembered her guests downstairs. Smirking, her mind drifted off as her imagination started to run with the possibilities.

 _We can get more water in the morning._

Shaw headed back toward their bedroom with a smile plastered on her face. As she entered the room, she tilted her head, frowning.

 _No lights. I thought Root was getting up to use the bathroom._

Shaw headed for the bathroom and turned on its light. Glancing toward the bed, she noticed Root was lying sideways as if she'd passed out. A ribbon of concern wrapped itself around her heart as she approached the bed.

 _Oh no, after what she's been through._

Shaw climbed on the bed and leaned down over Root's head. As she was checking her condition, Root's eyes snapped open.

"What are you doing?"

"What are you doing?" Shaw's voice was harsh, covering her concern ( _panic?_ ). "I thought you were getting up."

"I am getting up." Then realizing the position she was in, "At least I thought I was getting up."

"Are you OK?"

"Yes, Sam, I'm fine…. just a little tired."

Shaw looked down at Root, noticing how pale she appeared. Her concern ( _panic_ ) threatened to ratchet up into something approaching fear as she thought how much her love had been through in the last year.

She was:

Psychologically scarred from Shaw's captivity,

Shot,

Dead on a slab in a morgue (if only for five minutes),

Comatose for months,

Given a heart transplant followed by months of recovery and rehab all leading to the events of the last few days...

Where she was:

Tased,

Abducted and...

Tied to a cross by that piece of shit and his minions.

 _What the hell have I been thinking? She's been through enough to kill five people and we just hosted a dinner party…. after an hour of…. of… well intense activity. Then more intense activity... Shit, I've allowed my feelings to override my common sense._

 _This stops now!_

"Root, in the morning we're going back to the hospital and you're getting more than a brief session with Dr. Tillman. I've had my head up my ass regarding your condition and that's done, over, finished as of right now!"

"Sam? What's…."

"No! We are going to get you looked at, tested and given a clean bill of health. Or, you're going back in there until you have one. I said this before and I'll say it again. I won't… I _can't_ lose you Root. I lost you once… no... it's not happening again!"

Shaw wiped angrily at her eyes, shook her head and grabbed Root by the shoulders.

"We're going back this morning and that's final!"

Root looked into Sameen's eyes. Recognizing the concern and, yes, the love, she capitulated. With a small smile, she raised up and kissed _her_ love on the cheek.

"OK, Sam, you're the boss."

Shaw rolled her eyes. _Who are you?_

"Good, let's get back to sleep. We have a big day ahead of us."

….

Four hours later, Shaw was in the kitchen making pancakes, sausage, eggs, bacon and toast.

 _I should probably make something for Root and our guests._

She opened the fridge and pulled more supplies and set to work. Fifteen minutes later she went to the bedroom to check on Root. The bed was empty, but the bathroom door was closed. Shaw knocked softly on it.

"You OK, babe?"

"I'm fine, Sam, I'll be out in a minute."

"Why don't you climb back in bed, I made us breakfast."

"You say the sweetest things, Sameen."

Shaw turned back to the kitchen as the flush crept up her neck once again. Returning in moments with a tray filled with coffee, juice and some food, she found Root sitting on the side of the bed.

"You're almost as pale as last night. I'm glad we decided you are going back today."

"Are you sure this is necessary, Sam, I think I'm just tired."

"You know Root, there's a few things you need to realize. I've told you them before and I will tell you them again- and I will keep telling you them until you get it through that thick skull of yours.

"You're a warrior. You will rush into a hail of bullets with absolutely no regard for your safety. You showed how even the Machine better be careful or it will feel your wrath. You'll go days without food or rest when you're on a mission.

"Your feelings are so intense it scares everybody at times, yet you seem to think little, if anything about yourself. Your devotion to me, the Machine and the team borders on scary at times- but you treat yourself with such little regard it's almost as if you had a death wish.

"That's where I come in. Since you won't care for yourself, I have to watch out for you. And it's a labor of love, believe me. But it would be a lot easier for both of us if you would show just a sliver of concern for yourself the way you do for me and some of the others."

Root looked up with a faint smile.

"I love you, Sam."

Shaw's eyes softened and she leaned down to kiss the top of Root's head.

"Eat."

….

Almost an hour later, as Shaw was sitting at the breakfast bar drinking her third cup of coffee, Elizabeth walked into the kitchen. Shaw took one look at her and smirked.

"Sleep well?"

Elizabeth had the good grace to blush. She glanced over her shoulder at the stairs to the basement and said quietly.

"She's on her way up. Just don't say anything about last night. I wouldn't mind if there was a repeat performance in the future."

"I need to talk to her, and it's not about your social life so don't worry. There's food in the oven, and in the microwave. You guys are welcome to finish it, Root and I already ate."

"Right now I need tea. Then food."

Just then, Dr. Tillman appeared. Shaw, smiling, greeted her warmly.

"Dr. Tillman, good morning. There's breakfast for you both in the oven and the mic. Coffee's in the container next to the Keurig. Did you sleep well?"

The doctor's eyes were sparkling. She smiled and glanced at Elizabeth.

"I slept wonderfully. I'm not even hung over, which quite frankly, is surprising."

Elizabeth turned from the counter, tea in hand.

"Hey Megan, you want some coffee?" Shaw noted the use of her first name.

Dr. Tillman smiled and nodded. "Black please. Can I get you a plate?"

Shaw, amused by their interplay, decided to leave them alone for awhile.

"You two go ahead and enjoy. I need to take a shower then I need to talk to you doctor. I'm concerned about Root."

"What about Ms. Groves?"

"Let's wait until you're done eating and I've had my shower, then we'll talk."

"Fine."

Leaving the two alone, Shaw headed for the bedroom.

….

After showering and dressing, Shaw returned to the kitchen. Root, having finished breakfast was coding in bed with a cup of coffee on the nightstand. As she entered the kitchen, Elizabeth and the doctor were sharing a laugh as Dr. Tillman rested her hand on Elizabeth's knee. Smiling, Shaw cleared her throat and headed to the coffee maker. The two, looking like kids caught in the cookie jar, jumped up and separated.

Dr. Tillman, recovering quickly, looked at Shaw and smiled faintly.

"Breakfast was delicious, Ms. Shaw. What did you want to talk about regarding Ms. Groves?"

"I think we've all overestimated Root's physical recovery. She's probably the strongest person I've ever met, so I think she can do things that normal humans can't. While true much of the time, I think I've forgotten that she's still human. Last night, she was almost convulsing in bed while she slept.

"When I woke her up because I was terrified of the way she was shaking, she said she had a nightmare. I walked in here to get us a couple of bottles of water while she went to the bathroom. When I returned, she had passed out without getting completely out of bed and when I tried to check her out she didn't even realize what had happened.

"I told her she was going to get checked out completely and if she had to stay in the hospital until she got a clean bill of health, so be it. The thing about this conversation that scared me the most was that _Root didn't argue with me._ She folded without much discussion at all.

"That tells me she knows something is off, maybe she's even known it for awhile and wouldn't admit it to anyone, even herself. My calling it out may have just been what she needed to agree to get some help.

"I'm worried there's something seriously wrong with her, maybe even that she's rejecting the heart."

Shaw's eyes filled when she voiced the fear that had been gnawing at her. She turned her head, then looked back defiantly at both Dr. Tillman and Elizabeth.

"I told her I can't, I won't lose her again. I know that's extreme, but when I escaped from Samaritan we had a confrontation in the park. I threatened to kill myself, believing that was the best way to keep her and the team safe. She pulled her gun and said if I die, she dies. She said if I couldn't live with her, well she couldn't live without me.

"Now the shoe's on the other foot. I can't live without _her._ " Tears leaked out and cascaded down her cheeks as she stared at them. "You need to see if she's ok... you need to make her ok."

Shaw turned away, grabbed her coffee and stared out the window. As they watched, Shaw's shoulders began to shake. Elizabeth walked over to her and put her hand on Shaw's shoulder. Turning her gently, she took the coffee cup and wrapped Shaw in her arms. For several minutes Elizabeth held Shaw as she let out some of the stress and angst that had been building since early that morning.

When Shaw regained control, she leaned back, smiled at Elizabeth and sighed.

"Thanks."

"Shaw, Dr. Tillman is one of the best docs around. The hospital is one of the best in the world- the Machine made sure of that. Root's in the best hands anyone in her situation could possibly be in. Plus, she has _you._

"When I first came out to help my mom, that last part would have meant nothing. You couldn't have helped her, you couldn't have been there for her. Now you're different. I saw you at the church, you're still as dangerous as ever to your enemies. But with your friends, especially with Root, you're another person.

"Loving, caring, considerate, protective. As long as she has you to look out for her, I believe she'll be OK. And Root, she's changed too. Some of it's still there, let's face it: crazy's gonna crazy. But for the most part she's… and I can't believe I'm saying this, she's become more normal.

"She'll do what's necessary to get better, if not for herself, for you and Gen."

Dr. Tillman took the opportunity to interject.

"Ms. Shaw, we are going to find out what, if anything is bothering Ms. Groves. Everything Beth said is not only correct, most importantly that you're probably the biggest reason we are here. Without your presence, we might still be waiting for _both_ of your friends to return.

"You insisted on trying the experimental ultrasound procedure on her. I don't think it's coincidence that she first awakened within twelve hours of it. You went to New York to get John's friends here which played a huge part in his return.

"I can get the top physicians in their fields here to examine Ms. Groves if needed. Our facility is the best as is our staff. There is no place she'd be better off. There are several possibilities regarding Ms. Groves issue last night- most of them relatively benign.

"Whatever it is, we'll find it and we'll do everything possible to fix it."

Shaw's face had cleared and she smiled at her friends.

"Thanks again. So when should I bring Root in?"

"I'm clearing my schedule for today. Why don't we meet at the hospital in two hours…. say 12:30."

"We'll be there."


	3. Chapter 3

Root was giving Sameen grief- again. As they pulled into the hospital's main entrance, Shaw called reception and ordered a wheelchair. Root scowled at her and folded her arms in defiance.

"I can walk, Shaw, I'm not a cripple."

"Please Root, humor me. I would like you to ride in it, not because you're too weak to walk but because I just want you to. It makes me feel better OK?"

"Fine." She was _not_ happy about it. As Shaw pushed the wheelchair into the main reception area, Dr. Tillman was walking over to greet them.

"Hi you two. Where's Gen?"

Root smiled up at the doctor. "Gen went over to the kid's area, thought she'd see if any of them wanted to code awhile."

"That girl seems to be enjoying being a tutor."

"We keep telling her she could be a teacher someday. But she seems bound and determined to follow in Sam's footsteps- she wants to be a spy."

Dr. Tillman frowned, "I think I'd rather she be a teacher."

Shaw tilted her head.

"Ya think?"

"Let's head toward my office. I'd like to go over a few things with both of you before we get started on Ms. Groves' exam."

"Why do I feel like the condemned woman being led to her execution?" Root rolled her eyes and smirked, taking some of the sting out of her comment.

"Don't babe, just don't OK? This is just for my peace of mind." _I hope._

"Fine, let's get it over with."

The three women headed down the hall to the secure area and followed Dr. Tillman to her conference room. As they entered, they noticed a box on the table filled with papers. The doctor waved Shaw to a chair near the box.

"Most of the records are on computer, of course, but we took some notes by hand during your time before you awakened from the coma. I haven't had a chance to go through everything, but I've started looking at the protocol we devised during the post transplant period and there are a couple of red flags.

"I don't understand how it happened, but the normal dosage of anti-rejection medication was somehow replaced with an odd combination of drugs and supplements that should never have been used. It's almost as if the anti-rejection medication was eliminated completely.

"We were so busy with other components of your treatment this went unnoticed. When a drug is prescribed and added to a protocol, the computer automatically provides a daily menu of medications and a timetable for delivery. Sometime between the initial ordering and the production of the menu, the protocol was altered.

"I'm concerned about Ms. Groves' potential rejection of the donor heart, and I want to immediately biopsy it so we can check for any actual sign of rejection."

Shaw sat in stunned silence. _Oh God, what if she rejects the heart? Can we get another one? What do we do?_

Root looked at the doctor, expressionless. She suddenly lost focus and Shaw sat forward with a start. The Machine was talking to both of them.

 _I need to tell you something- including Dr. Tillman. We could use an earwig, but we can do this on a phone if we must._

Shaw, pulled a box from her jacket pocket.

"Before she left, Elizabeth gave me this back. It's her earwig doctor, we use them to communicate with the Machine. She wants to talk to all three of us."

Shaw held out the box and instructed the doctor on its use. The doctor looked at it suspiciously, then shrugging, put in the earwig. Following Shaw's instructions, she activated it.

"So what happens now?"

 _Can you hear me doctor?_

"Oh. That's strange, it sounds like a mixture of voices, both human and artificial. Yes I can hear you."

 _I hoped this wouldn't come up, but now that it has, I want to assure you, Analogue Interface isn't rejecting her heart._

"Who?" Dr. Tillman looked confused. Shaw shook her head.

"That's what she calls Root. Root initially was the only one who actually talked to her. I think it made Harold feel funny, since he built her.

"And how do you know she's not rejecting the heart, Machine?"

 _Because it's her heart._

Dr. Tillman shook her head.

"No it's not, I assisted the procedure- well mostly observed. I felt like a first year med student again, but you were my patient and I wasn't going to not be in there for this. I watched the surgeon remove your damaged heart and place the donor heart in.

"Your machine is wrong, it's not her heart."

 _I was really hoping we wouldn't have to discuss this…. I need to explain what happened so you don't expose Analogue Interface to unnecessary risk with biopsies and anti-rejection drugs._

"What are you talking about?" Shaw's voice was raising as she tried to keep from losing her temper. "What _happened_?"

 _Analogue Interface received a heart that was 'cloned' from her DNA. It can't be rejected because it's an_ ** _exact_** _duplicate of her original heart._

There was a stunned silence in the room. The three women sat looking at each other like they had just encountered an alien. Dr. Tillman was the first to recover.

"How did this happen? Do you know the ethical implications of this? What gave you the right to do something that's been forbidden by almost every medical association in the world."

 _The fact that something is forbidden doesn't mean it isn't done, doctor, you know that. There already are several small clinics around the world doing experimental work cloning humans for various reasons._

 _I simply accessed the most successful one and put it to use for assets._

Shaw stood, then realized the gesture was probably lost on the Machine.

"What do you mean assets? What have you done? Are you growing replacement parts for all of us?"

 _Very astute Ms. Shaw. That's exactly what has been done, and it was fortunate that it was started before the need arose- Analogue Interface needed a heart within two weeks of it being fully developed._

"OK, look, can you call her Root, or Ms. Groves. I'm sick of the impersonal way you describe the only reason you still exist. Without her, you'd be a bunch of transistors and capacitors in some electronics store. Or just junk."

 _No need to be rude Ms. Shaw, but I will be happy to call her whatever she wishes._

"Root works for me." Root looked shaken and not a little displeased by the information they had just received.

 _Most complications regarding heart transplants occur as a result of either rejection or the process used to prevent rejection. Damage to the organ itself, disease and cancer mostly from the fact that a foreign body has been introduced. This hasn't happened in Root's case- there are no possible rejection issues._

 _There are possible issues with the procedure itself since none are done to perfection. There are possible issues with infection as well, since no environment is totally sterile. There are possible issues with her activities since the procedure._

 _There are no issues regarding Root rejecting her heart._

The Machine lapsed into silence.

Dr. Tillman frowned. "There are non-invasive testing procedures we can use to determine if DNA from the heart matches her overall DNA. I'd like to order that immediately. You'll forgive me if I'm skeptical of the Machine's claims."

Shaw stood and began pacing. "I'm skeptical of the Machine's sanity… at the very least, I think we need Harold and Root to run diagnostics on her to see what went wrong. There are safeguards that were to prevent….. oh."

Shaw looked at Root.

Root was staring off into space. She looked down then brought her gaze up to Sameen.

"OK, Sam, we may have to get Harry over here to discuss possible glitches in her moral compass." The words rang hollow, even to Root.

"She's a machine, Root, the only _moral compass_ she had was removed months ago. Harold warned us about this, and it's starting to look like he might have had a point."

"I'd love to disagree, Sam, but I'm afraid you may be right. Do you want to call him, or should I?"

Shaw's phone was already out.

"Hi Harold, we are down in the conference room by Dr. Tillman's office. Can you join us ASAP? There's a situation we need to address… Fifteen minutes? Sounds good.

"He'll be down shortly." Shaw looked at the others as she put her phone away. "Dr. Tillman, how long does the test take to determine if the Machine's claims about her heart are true? And can it be done quickly without risk to her?"

"We run blood work and take tissue samples with every patient and procedure in this facility. I can simply run DNA tests on the donor organ from tissue samples we gathered when we first received the organ.

"As you might expect, time was of the essence when the heart arrived…" Dr. Tillman's gaze left the ladies as she recalled the circumstances, "in fact, the timing was almost too perfect to be true- which leads me to believe it was done so our matching would be less detailed than any of us liked.

"If your machine had given us even an extra hour, we could have done a preliminary DNA test to determine risk factors and other possible issues. Instead, we did a quick typing match and forged ahead in an effort to prevent your death, Ms. Groves…. Root.

"That test might have raised red flags if it showed what the Machine says our test will show, that it's a _perfect_ match as opposed to an acceptable or ideal match. Usually ideal matches in situations of organ transplants involve family members.

"I'd rather not speculate any more until we have more data. The test results will be available in less than 24 hours. We can either confirm or dispute the Machines claims in less time than normal since we are looking for one particular match rather than a process of elimination."

Dr. Tillman said this while looking at her phone. Within sixty seconds she looked back up at Root and Shaw.

"It's ordered, and they know to put it at the top of the priority list. We can start a series of tests designed to isolate Root's symptoms and see what is the cause. I'm afraid she will have to spend tonight here though, we can't do some of the tests until the DNA match is complete."

"Why can't I just go home tonight and return first thing in the morning? I appreciate all you've done here for me, but I'd rather sleep in my own bed, get a good night's rest and come back. I sleep better at home."

Dr. Tillman nodded toward Root. "That would be acceptable as long as you're willing to forego any strenuous activity until we determine an appropriate treatment protocol for whatever we discover is affecting you."

Root rolled her eyes and glanced at Shaw who was gazing back at her. "Whatever."

Shaw's smile started to creep across her face. "Come on Root, we can take it easy for a few days."

Root stared at her, then smiled. "Hey, I was in a coma for six months, I've got some making up to do."

"Am I interrupting something?" Harold entered the room and approached the conference table.

All three started to speak, then stopped. Shaw looked at Root, then at the doctor. Both nodded back at her, and she began.

"Harold, it appears we have an issue with the Machine." Shaw explained the situation, Root's potential problems and what the Machine revealed about her heart transplant.

"The good news is, assuming the tests confirm it, Root will never have an issue with organ rejection. Since rejection and the complications arising from attempts to prevent it are what shortens expected life spans of recipients, she has a long life to look forward to. Which she'll probably use to annoy us with."

Shaw smiled and winked at her love. Root stuck her tongue out in response.

"The bad news, is our concerns about the Machine and its lack of inhibitions. It indicated that it had little if any problem with unrestricted cloning as long as the ends justified the means. We had a discussion weeks ago about potential negative consequences of removing any restrictions you originally built into it.

"You were the one who expressed reservations about the possibility and, after some heated discussion, we tabled the issue. We think it may need to be addressed and dealt with now."

Finch looked over at Root. "Ms. Groves is the one who was the Machine's staunchest defender as I recall. Are you telling me she's in agreement on this as well?"

Root looked down, then back at the group. She was quiet for an uncomfortably long period, then she took a deep breath.

"Look, I'm still alive because of her. Everything that was done to save me was set in motion by her. I was in awe of her before this. Hell, I was in awe of her before Samaritan even existed. A part of me _loves,_ for lack of a better word, her.

"In spite of that, I realize we can't let her go on without establishing some boundaries. This situation has convinced me that my original view that things would be fine without tweaking her was wrong. I thought she was smart enough to realize the need for morality.

"Maybe morality can only be instilled by a creator."

Root looked up at Harold,

"Can it be done Harry? And if so, how do we do it?"


	4. Chapter 4

Finch considered the question for several minutes. When he finally responded, it was with the care and precision that used to drive Root crazy. This time though, her shock at what the Machine had done tempered any objections she would have raised.

"We can reboot the Machine's 'safeguards' in a relatively short period of time. I would think that the two of us working together can code the appropriate lines in within a two to three week time period. We may be able to shorten the lead time if we bring Ms. Zhirova in to assist us- she can help with some of the simpler steps which can free us up to work on the more complex protocols necessary to reinstate a 'Code of Conduct' for lack of a better term.

"After we initiate the new protocol, we will have to monitor the Machine's more complex decisions whenever moral and ethical issues arise. The troubleshooting phase would be less intense but probably more time consuming as we analyze how and why certain decisions are arrived at.

"A rough guess would be four to six weeks and then monitoring for several months until we can reach a consensus that our safeguards are working to our satisfaction. The tricky part will be allowing the Machine to continue to provide numbers while undergoing, for lack of a better term, brain surgery."

Root leaned forward. "Can we do that?"

"It will be expensive but it can be accomplished. One of the advantages to the Machine's being a 'machine' is that it has no emotions. It won't be upset that we're putting in these safeguards- it has no pride to fight us on this. When left to its own devices, it may make decisions we view as morally objectionable, but it still has core functions which will direct it to follow 'Admin' instructions.

"I view those functions as similar to autonomic nervous system functions, like breathing, heartbeat and digestion. Our body continues to do these things, unless outside factors interfere regardless of our state of mind or moral code. We can create an exact copy of the Machine even though it will be expensive, work on one copy while allowing the other to act as it has been since the war with Samaritan ended and it rebooted itself.

"Once finished and tested to our satisfaction, we can implement replacement protocols. We would in effect clone the Machine and 'transplant' a moral code. That analogy is a bit of a reach, but the result would be similar."

Dr. Tillman jumped in.

"This is all well and good, but our first priority is getting Ms….getting Root a clean bill of health. Tomorrow she will be back and there are several tests we are going to run on her. Assuming all are negative, we can discuss working on fixing your Machine's conscience after we assure ourselves that Ms. Gr…. Root is not suffering from any condition that need immediate action."

"Thank you doctor," Shaw affirmed, "Root's condition and long-term prognosis are my main priorities right now. I agree we need to fix the Machine, however first I want to ensure that we're going to have her around long enough to have second thoughts." She smiled at this last, and walked over to Root and wrapped her arm around her neck.

Root smiled up at her and made a kiss-kiss noise. "I love you too, Sameen, enough to agree to this when I'd much rather skip the tests and go to work on the machine."

"Good, let's go home and come back in the morning." Shaw grabbed the handles of the wheelchair and turned Root toward the door.

"I can walk Sam."

"Let's get the test results first, OK babe. I love you and want to keep you around for awhile yet."

"Sure, play the feelings card." Root smiled and winked.

Shaw's heart did that thing.

….

The next morning at 8:30 Shaw pushed Root through the entrance with Gen trailing behind. They headed straight for the examination room where Root changed into a gown. Five minutes later, Dr. Tillman entered the room.

"DNA tests confirm what the Machine told us yesterday Root, you have a heart that is an exact genetic match for your body. I've put any anti-rejection protocols on hold for the time being and we are going to perform other testing to see if there are any issues that could have arisen from other factors.

"We'll test the organ as it relates to the transplant procedure itself, the possible complications from the several weeks after that you were comatose, the post awakening rehab and of course your activities since leaving the hospital. Unless critical, any issues we find will be dealt with after we have appraised, isolated and prioritized them all.

"The first step will be the transplant procedure itself. To evaluate, we are going to run a series of tests including EKG, Electro-cardiogram as well as an ultrasound of the organ itself This will allow us to judge if any issues from the procedure are affecting the heart's performance.

"Once finished, we are going to take you into the OR for a heart catheterization. We'll run a probe from your groin up into your thoracic region to get a better idea of how your arteries and heart are actually functioning.

"There is a possibility that scar tissue is forming within the arteries and veins surrounding the heart. This will allow us to view the entire area and repair any blockages. The entire procedure should be less than an hour, and you'll be ready to leave sometime this afternoon.

"Once we've examined your heart and the arterial structure surrounding it, we will decide what we need to do next."

Dr. Tillman busied herself setting up the equipment for the non-invasive procedures. Shaw sat with Root in an uncomfortable silence. Finally, Shaw reached over for Root's hand.

"I'd like to stay, but if you'd rather have privacy I'll leave."

Root, visibly moved, smiled. "Stay."

Shaw stood next to her love, holding her hand until the doctor announced she was ready to begin. Sameen then leaned down, kissed Root briefly and walked to a chair brought in for her by staff.

"You know how this works Ms. Shaw, you've probably done dozens during your medical career. I will be monitoring the results while the techs run the actual procedures on Ms….Root. Sorry, I'll get used to calling you that." She smiled and nodded at the patient, then turned and moved over to the battery of monitors she would be studying.

Everything went as planned for the first 20 minutes. When the ultrasound began, Dr. Tillman made a phone call and was joined by a mid-forties man she introduced as Dr. Miles Brady, a cardiologist from Houston.

Shaw was going to ask why he made the trip all this way, then decided against when she realized the Machine probably ordered the top doctors from the area to work with Dr. Tillman on the 'Analogue Interface'. While the ethical issues were still a concern, Shaw trusted the Machine to keep Root safe.

Before Dr. Brady approached Root, Dr. Tillman introduced him to Shaw. He smiled warmly as they shook hands.

"I don't know who your friend is, but someone very important wants her to get the best medical treatment available. I'm good at what I do and as I arrived last night, I ran into Dr. Joseph Ryan, the best Thoracic surgeon in the southwest, if not the entire country.

"It turns out he was offered an obscene amount of money to come in for a consult on Ms. Groves here just as I was. I've read many of Dr. Ryan's papers and if I, or anyone in my family, were to have any thoracic issue I'd want him to be involved in the treatment.

"Someone thinks very highly of her."

Shaw smiled at the doctor. "Many in this building think highly of her, doctor. She's the most important person in my world. Thank you for coming and thanks for the encouraging words."

Dr. Brady nodded, then approached Dr. Tillman.

"Let's get started." The two approached the examination table where Dr. Tillman introduced Root.

"Root, this is Dr. Brady. He's going to do the ultrasound of your heart. He's the best cardiologist in the United States, probably in the world."

Root nodded at Dr. Brady.

"Pleasure to meet you, Root. I'm going to begin by doing an ultrasound of your heart. We should be able to see not only how the organ itself is functioning post-op, but also check out the entire area that was affected during the surgical procedure. If any abnormalities show up, we will address them after the entire procedure is finished.

"It should take about thirty minutes for the entire exam, then we will perform the catheterization which will require sedation. You've already signed all the consent forms, however I want to briefly review what you've agreed to before we begin.

"If at any time we encounter an issue that needs any type of critical care, up to and including surgical procedures, we will initiate them immediately. Any non critical procedures or follow up treatments will be done after consult with you and your immediate family."

Root interrupted, "My immediate family is in that chair." She smiled and Sameen smiled back.

"Noted. Let's begin."

Shaw's attention wandered from the doctors to the monitors periodically, but her main focus never strayed from Root for more than thirty seconds during the fifteen minutes that everything went as she expected. As part of her residency, Shaw had done a three month rotation in cardiology so she was familiar with what Brady was doing.

At approximately the fifteen minute mark, Shaw noticed a small change in both doctors affect. Dr. Brady looked at the monitor, looked at Root then looked at Dr. Tillman.

"I'm going to go back and check that again."

Dr. Tillman nodded and Shaw came to full attention. Wanting to ask what was happening, she knew enough to keep quiet while they looked at whatever was a cause for concern. The two doctors looked at each other, their concern obvious in their body language. Dr. Brady looked at Root, then at Dr. Tillman.

"Once more."

Shaw, unable to control herself any more, cleared her throat. Dr. Tillman looked over and held up her hand with her index finger pointing up.

 _Just a second._

Less than two minutes ( _an eternity_ ) passed before Dr. Ryan turned to Shaw and indicated she should approach the examination table. Turning the screen so both Root and Shaw could see it he indicated an area on the monitor. As they looked at the monitor, Dr. Tillman slipped from the room.

"This is the area where the aorta joins the heart. Traveling back along the aorta we have this area that causes concern." Dr. Brady indicated an area which to Shaw looked to have a slight bulge. Root was unable to discern any difference but she had no medical training.

"It appears that Ms. Groves has an aortic aneurism, probably caused by the trauma of the heart transplant she underwent. As you know, Ms. Shaw, the patient is on a heart lung machine during the actual transplant and there are moments when blood flow to the organ is interrupted. This appears to have resulted in a weakening of the aorta in this location.

"The strain is causing the wall of the aorta to bulge. Untreated, this can and will rupture sometime in the future. If that occurs, death is almost always the immediate result. I'm concerned that the aneurism is large enough that it needs to be repaired now. Dr. Ryan is coming in to… oh good, here he is."

As the door to the exam room opened, Dr. Tillman walked in followed by a very young man. At first glance, Shaw thought he looked like a grade schooler dressed up for Halloween or someone who got into his dad's closet. When Shaw looked into the doctor's eyes, she saw the intense piercing gaze of a man on a mission.

Nodding at Shaw, he approached Root.

"Ms. Groves, I'm Dr. Ryan. I want to recheck an area on your ultrasound, then we'll talk."

Five minutes later, Dr. Ryan looked up at Dr. Brady and nodded. His face relaxed into a warm smile and he addressed Root.

"Ms. Groves, somebody up there likes you. You have quite possibly the largest intact aneurism I've seen. Why it hasn't ruptured already is something we won't know until we get in and fix it. We need to repair this before it ruptures. I would advise the procedure be done today, in fact within the hour we should begin."

Root's eyes widened as the doctor's words sunk in. She looked briefly at Shaw and for a brief moment, Sameen could see fear in her eyes. Then, recovering, she masked any concern and looked at the doctors.

"Fine, I'm not going to put Sam through burying me if I can help it. Let's do this."

Shaw walked over, put her arm around Root and kissed her on the cheek.

"Well, these guys are the best, Root, you're going to be fine."

She wouldn't look Root in the eye.

"Do I need to get out of here so you can prep her?"

When Dr. Tillman nodded, Shaw kissed Root again and headed for the door. She walked across the hallway to the ladies room, locked the door behind her and promptly threw up.


	5. Chapter 5

Shaw stayed in the bathroom for several minutes composing herself. Then, once she felt in control, she waited outside the examination room until the doctors wheeled Root out to head to surgery. She put one of the biggest fake smiles on her face and approached the gurney. Leaning down she once again kissed Root on the forehead and brushed a lock of hair from her face.

"I'm calling Harold and John to let them know, but I'm going down to talk to Gen in person. We'll be up in the observation deck watching."

Root shook her head.

"I'd rather you weren't, and I want to ask you to specifically keep Gen out of there."

"Why, babe?"

Roots face twisted slightly. Tears shone in her eyes.

"I love you Sam and if something happens, I don't want you to have to see it. It's one thing to watch someone you love riddled with bullets saving your life, it's another to watch something like this. I died some that day at the Stock Exchange, and wasn't able to recover from it until you were back safe with me.

"If something happens on that table, I don't want you to have to look on helplessly- I know what that feels like and it sucks. And Gen's just a kid. I really think I'll be fine, but just in case."

Shaw's shoulders were shaking and she was right at the point of losing control. As tears cascaded down her cheeks, she hugged her love and whispered.

" _You have to come back to me_."

Then standing, she smiled through her tears.

"I love you, Root. I'll be waiting."

She followed the gurney down the hall with her eyes and waited until they disappeared around a corner. She then called John and Harold, spoke to each briefly and headed down to where she knew Gen was working with the kids again.

Despite Shaw not being the praying type, she couldn't help her eyes as the went toward the ceiling.

 _Please let her be OK!_

….

Shaw found Gen coding with some of the Native American kids. She watched for several minutes trying to enjoy the fact that more and more Gen appeared to truly relish her role as tutor to these kids. Her mind kept drifting to Root and what was going on up in the O.R. When Gen finally looked over and noticed Shaw, she came over and instantly knew something was wrong.

"What's going on Shaw? You look… well if it was anyone else, I'd say you look scared. What's got you so shook up?"

"When they ran the tests on Root they found an aortic aneurism. It's pretty serious and they took her right up for surgery to fix it. I'm just worried that _she's_ scared."

Gen looked at Shaw skeptically.

"I don't know, Shaw, how serious is it? You look like you're not telling me something."

"Gen, I can't lie to you. It's serious and yes, I'm concerned. But the best guys in the world are working on her so I have to be confident that they can fix her. We just have to wait and let the doctors do their thing."

"Where are we waiting? Are they doing it in that room we watched?"

"I'm not sure, I promised we'd all wait down the hall until Dr. Tillman had something to tell us."

The two walked toward the waiting area lost in thought. When they arrived, John and Finch were already there. John stood when Gen and Shaw entered and looked Sameen over, his concern obvious.

"How are you doing?"

Shaw took a deep breath and let it out.

"I'm scared, OK? But she's in the best hands possible. I just have to believe she's going to be fine."

They all stood around silently for several minutes. Shaw suddenly looked at John.

"I have to call Elizabeth."

She walked out of the waiting area and pulled her phone out. Elizabeth answered on the first ring.

"Talk to me, how is she?"

"She's in surgery… she's got an aneurism… it's serious but they're hopeful they can fix it and…"

Shaw's voice failed and for the next few minutes Elizabeth could hear Shaw crying uncontrollably.

"I'm coming back."

"No, Elizabeth, you can't do anything here."

"I can be there with you. I was going to come back anyway and bring my mom soon- Megan said she'd have the best neurologist in the country take a look at her, then bring in any other specialists needed to get her back to normal. This is just a little sooner than I planned.

"No arguments, we'll leave this afternoon and be there by nine at the latest."

"Thanks Elizabeth."

"Hell, Shaw, if this thing with Megan works out, I'll owe you big time. This is nothing."

Shaw smiled into the phone and felt a little of the fog lift.

"See you tonight" the two said almost simultaneously.

Shaw walked back to the group smiling.

"Elizabeth's coming back and she's bringing her mom."

John looked surprised.

"I didn't know they were at that stage."

Shaw looked at him, confusion written on her face. "What?"

"She's bringing her mom to meet Dr. Tillman, that implies they must be serious."

Shaw's laughter filled the area- she was genuinely delighted.

"Oh John, thank you, I needed a little humor."

Reese looked offended.

"I'm glad I can amuse you, Shaw."

"No, John, I'm not laughing at you, I'm just laughing at the thought that Elizabeth and Dr. Tillman thought they were being subtle. Besides, she's bringing her mom because Dr. Tillman is going to have Dr. West take a look at her.

"Although, now that you've mentioned it, maybe there's more to it than just a medical consult. And she's coming tonight instead of later to be here with us and for Root. It's really sweet."

….

The time crawled by. Root had disappeared into the elevator around 10:30. By noon, Shaw was beginning to get stir crazy. She was familiar enough with what was being performed that she knew it could take as long as eight hours depending on what they ran into in Root's chest.

Gen had wandered back to work with the kids, probably to take her mind off Root, while Harold sat alone working on his laptop doing preliminary workups on the Machine's possible lobotomy.

John had headed down to the Health Complex to continue his physical rehab, which was progressing nicely. He was starting to grumble about being kept "in jail" and was campaigning to be released.

Shaw was left to her thoughts and she watched the clock on the wall crawl through the hours. _Breathe Shaw- she's in the best place for what's gone on. She'll be fine…. what am I going to do if something goes wrong? Breathe Shaw- Dr. Tillman brought in the two best possible docs to work on…. what am I going to do if something goes wrong? Breathe Shaw- this facility is the best in…. what am I going to do if something goes wrong?_

Shaw started as she felt a hand on her shoulder. She looked up into Dr. Tillman's face. Over her shoulder the clock showed it was just after 3:00. She knew she'd never forget the moment.

Dr. Tillman took Sameen's hand in hers. The doctor's eyes danced as she squeezed it.

"The surgery went fine, Root's going to be OK."

Shaw held onto the doctor's hand and wept.

….

Gen came rushing into the waiting area grinning from ear to ear.

"Ha! I told you before Shaw, you guys are _indestructible!_ "

Shaw rolled her eyes and hugged Gen. Harold and John were standing around smiling. Shaw's eyes were red from crying but her smile showed both joy and relief. She had told Dr. Tillman that Elizabeth was on her way with her mom and the doctor blushed and smiled. ("I look forward to meeting her.") Then she left the room to check on Root.

Shaw pulled out her phone and called Elizabeth. After shouting "Yes!" she assured Shaw she was still coming and was on track to arrive a little early.

"You better, Elizabeth. I told Dr. Tillman you were coming- and she was pleased to say the least."

"Be careful Shaw, I may be walking a tightrope here. Mom's sleeping but I have to be careful and get her used to this slowly. She's not a prude, but she is from a different generation."

"You'll be fine. Your mom will be cool. I've seen her offspring, there's a lot of substance there and I know she'll be happy if you're happy."

"You're sweet Shaw, I'll see you in a few hours."

….

By 6:30 the anesthetic was beginning to wear off. Shaw, who had planted herself next to Root's bed and announced she wasn't moving until Root woke up and talked to her, was holding her love's hand and carrying on a one way conversation.

"So I called Elizabeth went you went in and she's on her way. She's bringing her mom so they can check her out here. The timing is odd but she wanted to be here to support you, me and Gen. She also, I think, wants her mom to meet Dr. Tillman, which I think is cute. It also tells me Elizabeth sees our doctor as more than just a fling…"

"They'd be good for each other…" the words came out whispered, but shocked Shaw as if they'd been shouted. She stood and kissed Root lightly on the forehead. She reached for the call button.

"I want the doctors here right away… she's awake.… I will call Dr. Tillman." Shaw had met the nurse at the door to Root's room. As the nurse went to summon them, Shaw pulled her phone and called Dr. Tillman.

"She's awake, I sent the nurse to notify the other doctors."

"On my way."

…..

The doctors spent the next forty-five minutes examining Root and going over the operation and her prognosis. Hospital for a week during which time they would run several tests and procedures to ensure the aneurism was the only issue. Then bed rest at home for a week or two followed by routine exams every week until three months post-op.

Both doctors would be returning to Albuquerque at the three month mark to examine Root and hopefully give her the green light to resume all normal activities. To say Root was unhappy about the restrictions was an understatement.

"This sucks. I just got out of here a few weeks ago and now this? Why here a week? Why bed rest? Why three months? Why?"

Dr. Ryan answered.

"Ms. Groves… Root, you've just been through a procedure that literally saved your life. I've seen people who went through an aneurism repair spend a year getting back to their pre-op condition. Believe me, you're in the express lane on this.

"I still don't like the lack of medication re your transplant, but I've also seen the DNA matching data on your organ and to say this situation is unique is an understatement. I should be reporting this to the state ethics board, however my services here came with a non-disclosure agreement I signed before coming here.

"Now I'm beginning to see why."

Dr. Brady nodded and added, "I had the same requirement or I'd have already filed a report."

Dr. Tillman jumped in.

"Dr. Ryan, Dr. Brady, there are very good reasons for the agreements you signed. I would like you to understand why we put them in place- mostly so you understand that this facility and everyone you've encountered are not engaged in any unethical practices.

"Of course, this will all be covered under both the agreement and doctor-patient privilege. Let's go back to my office."

Turning to Root and Shaw, she smiled and winked.

"My turn to blow some minds."

Shaw reached into her pocket and removed the earwig. She offered it to the doctor.

"You know how to use it, if you need to provide them with any 'proof'.

Dr. Tillman smiled and nodded. She turned and left the room.

Root grabbed Sameen's hand.

"I think she's enjoying herself."

Shaw smiled but knew in the back of her mind, Root would be returning to the issue of her recovery soon.

 _I hope she understands how serious this all was and is. I may have to remind her… again._


	6. Chapter 6

Harold, John and Gen rotated through Root's room for the next hour or so. Gen seemed almost cocky, bragging about her confidence that Root would be OK. John said little, holding Root's hand as he smiled down on her lost in thought. _Who'd have believed we'd end up here, three stone cold assassins and a nerd, as close to family as you can get?_

When John hugged Root and left the room, Harold came in. He approached Root's bed almost shyly, unable to look her in the eyes. Root watched curiously as he cleared his throat.

"Ms. Groves…. Root….

".. Um…I can't put into words how happy I am that you're still with us….I've never really told you… how much… you've come to mean to me…

"Your passion for the Machine, the team….. and now your 'family'…. uh….. well…. has brought me closer to you than I ever thought possible…"

Faltering, he struggled, then looked into her eyes.

"I feel like you are the daughter I never had. I'm just so relieved…."

Finch's voice trailed off and he took Root's hand, overcome with emotion. Root, moved by the words she never dreamed she'd hear smiled up at Finch, eyes shining.

"Harold, you've always been like a father to me. I feel like so much of the struggles we've gone through are just me trying to get your approval. Knowing you care and accept me for who I've become is more than I could have ever expected.

"Now, let's talk about how we find and install a conscience for Her."

"I've started… I'd be happy to go over my ideas after you get some rest and we discuss this with the doctors."

Root stuck her tongue out at Finch, but her eyes sparkled.

"Fine." A slight smile threatened to appear. They were interrupted by Shaw's reappearance.

"I just got a text from Elizabeth. She's less than fifteen minutes away- I'm going to let Dr. Tillman know and head down to meet them." She smiled at the two of them, then walked briskly to Root's bed, bent down and kissed her forehead.

"Be back in a few."

….

Both Shaw and Dr. Tillman waited at the main entrance of the hospital. Shaw noticed the doctor appeared nervous. She tilted her head, curious, then as it clicked, reached out and took the doctor's hand.

"Relax doc, she'll love you. You two are going to be fine."

Dr. Tillman's eyes widened and a flush crept up her cheek.

"Is it that obvious?"

"Only to those of us who know you well. Just take it easy, be yourself and remember, Elizabeth's mom is going to be a patient first- then…. well then who knows?"

"I didn't know you also studied psychology Ms. Shaw. That's pretty insightful."

"I may have had the _feelings_ thing turned down all these years, but I've always been fairly good at observation. In my old line of work it came in handy….."

Shaw's voice trailed off and she raised her hand to her temple, wincing. Of course the doctor noticed.

"Are you alright?"

"Just a headache, I probably didn't get near enough caffeine today."

The doctor looked over at Shaw thinking, _I'm pretty good at observation as well, Ms. Shaw and that seemed a bit stronger than a caffeine headache._

Her reverie was interrupted by Shaw's pointing toward the drive.

"They're here."

And all thoughts of Shaw's headache vanished, and wouldn't return for a few days.

….

Elizabeth parked near the circular drive where patients were dropped off and popped out of the Excursion. She hurried around to the passenger's side, opened the door and helped an attractive late 40's woman out of the passenger seat.

Shannon Ruben was pale and had lost considerable weight during her long recovery from the accident that almost killed her, but her beauty was still obvious. She was a few inches taller than her daughter ( _wasn't everybody?_ ) but the resemblance was obvious. Less obvious to anyone meeting her for the first time were her eyes; dulled by the results of the near fatal accident, but when she was healthy sparkled with such life and beauty that men (and women) could get lost in them.

Dr. Tillman and Shaw approached the pair, Shaw beaming and Dr. Tillman still nervous. Elizabeth looked toward the pair and smiled.

"Megan, Shaw, long time no see."

She left her mother briefly to hug both women, Shaw first then the doctor. She lingered in Dr. Tillman's embrace for just a brief moment and the two shared a look that Shaw noticed immediately. Unknown to them at the time, Elizabeth's mom noticed it too.

"Megan, Shaw, this is my mom, Shannon. Mom these are two of the people I told you about, Sameen Shaw and Dr. Megan Tillman."

Shannon smiled at the pair and stuck out her hand. "Nice to meet you. Elizabeth says nice things about both of you."

Elizabeth looked at her friends. "How's Root?"

Shaw rolled her eyes. "Awake and already being a pain in the ass…. oops, sorry Ms. Ruben."

"I've heard worse- as a matter of fact, today, on the drive down." She glanced over at her daughter. Elizabeth rolled her eyes.

"Some people need to learn how to drive. Let's go in, I want to see Root."

The group headed into the hospital.

….

There were so many people in Root's room Dr. Tillman finally had to shoe everyone but Elizabeth and her mom out. After a few minutes, Elizabeth excused them and as she was leaving Root called her back.

"I like your mom, but she hasn't fully recovered has she?"

Elizabeth's smile faltered.

"No, and I don't know what to do to help."

"Can you ask Dr. Tillman to come back in for a minute?"

Root stared pensively at the window wishing she weren't cooped up in a hospital but glad she was still around. When Dr. Tillman re-entered the room, Root stared at her.

"I like Shannon, but she's still not fully recovered from her accident. She seems physically fine but still in a fog. Can I make a suggestion?"

"Sure, Root… go ahead."

"I know I'm not a doctor, but while I was in here I studied the file on me and also studied John's. It seems that we both were suffering more from our brain injuries than the physical damage done to us. It seems Shannon is in the same boat.

"I also studied the procedure you used on me and watched and familiarized myself with the holistic methods Dr. Ingram used on John. I know there were no, repeat no possible negative side effects or repercussions from either procedure.

"Why not try them both on Shannon to see if anything positive can come out of them. You could try one at a time then both together. They can't hurt her and we've seen the positive results they can have. There's no down side."

Dr. Tillman was silent for a good two minutes. She nodded her head slightly, smiled at Root and replied.

"That's not a crazy idea. I don't know if it would help, but I do know it won't hurt. I'll be conducting tests on her over the next couple of days and will bring both Dr. West and Dr. Ingram in to consult on her."

She looked at Root fondly.

"Thanks."

Root smiled and nodded.

"Hope _everything_ works out."

Dr. Tillman left the room with a slight flush creeping up her neck.

As she reentered the waiting area where Reese, Finch, Gen and Shaw stood talking with the new arrivals, she looked at Shaw and nodded toward Root's room. Shaw shook her head and indicated Finch and Gen.

"The two of them want to discuss strategy with Root before they start in on the Machine's brain surgery."

Dr. Tillman went over and spoke quietly to Gen and Harold. As they disappeared into Root's room, Shaw looked at the remaining four. Elizabeth and the doctor were stealing surreptitious looks at each other while Shannon pretended not to notice.

 _Oh that's interesting, these two have no idea how obvious they are._

When she looked at Reese it stopped her dead in her tracks. She had seen his flirtatious banter with Zoe, remembered his feelings for Joss which were cut short by her murder and seen him with Iris as they tiptoed around a relationship. She'd never seen him look like a lovesick teenager. But that's how he was staring at _Shannon_.

Recovering from her surprise, she walked over to Reese and said very quietly,

"John, your mouth's hanging open. Be careful, you might start drooling."

Reese snapped his mouth shut and shook his head. He looked down at Shaw with a small amount of red creeping up his neck.

"Not a word, Shaw."

"Don't worry, your secret's safe with me. You don't even know her."

"Yeah I know, and I _don't know_ what just happened." He motioned Shaw to move away from the three ladies. "I'm a little embarrassed but when I met her, something inside went, 'whoosh'. This is so weird- I don't do relationships, at least not since Carter died.

"But what happened a few minutes ago was totally out of left field. I think I should get back to my room and get my head back on straight."

"I'll see you in the morning John."

Shaw walked over to the door of Root's room and knocked lightly. Peeking inside, she saw Harold engrossed in his laptop while Gen sat by Root's side holding her hand. Root was on the verge of sleep and Shaw approached the bed, leaned down and kissed Root's forehead.

"I think Gen and I will head home Root. You look like you could fall asleep at any second. It's been a long day for all of us and we'll be back first thing in the morning. Love you.

"Goodnight Sameen."

Root's voice, obviously tired, still got to her. She turned and left without a word. Gen followed.

….

The next morning, Dr. Tillman had Root's suite altered to allow for more visitors. The group knew not to tire her out, but seemed to find comfort in gathering together. As they were quietly talking amongst themselves, they were interrupted by the appearance of Dr. West, the neurologist who had assisted in both Root's and John's care.

Dr. Tillman took Elizabeth and Shannon out of the room to meet the Dr. West.

"Dr. West, Shannon was involved in a serious car accident months ago. Her physical recovery is almost complete, but neurologically she seems to have lost some of the edge she once had. I explained to Elizabeth that you are the best in your field and that if anyone could assist her mom in a complete recovery, it was you."

Dr. West smiled and took Shannon's hand.

"I'd like to meet with you and go over some of your history- then we can schedule tests for you. I think we should start later this afternoon if that suits you."

Shannon smiled faintly.

"I know there's something not quite right. It's like I'm in a fog much of the time. I miss my old self- at least the part I remember. I can't wait to get started."

"Excellent, how about 3:00?"

Shannon nodded and Elizabeth smiled at her.

"She'll be there."

Dr. West excused himself, he had some other patients at different facilities. Shannon, Elizabeth and Dr. Tillman returned to Root's suite. They discovered chaos. Shaw was standing over Root, leaning down and holding Root's arms against the mattress. Finch and Reese were standing off to the side eyes wide.

"I _will_ zip-tie you to this bed, _do you hear me?_ "

"Whoa guys, what's going on?"

The two looked at Dr. Tillman and Shaw released Root's arms and spun around.

"So we're talking about her treatment and her helping Gen and Finch when we got a number. Root looks at me and tries to get out of bed and says, 'we've got to get moving.' I swear doc, this woman will drive me completely around the bend if she doesn't figure out that she's not going anywhere for the foreseeable future.

"I meant what I said, I _will_ zip-tie her to this bed if she doesn't cooperate!"

Root looked at Shaw, concern showing as her brief anger faded.

"Sam, you can't go out chasing numbers alone… you can't."

Shaw rolled her eyes and shook her head. Exasperated, she looked Root in the eye.

"Number one, I no longer go out alone. As you should remember, I have _Her_ in my head whenever needed. Number two, you would be more hinderance than help in your condition- even if we allowed it _which we won't._

"Number three, I would take John before you even though he's not ready to go out in the field yet because he's in way better shape than you right now…."

"And number four…" a voice came from across the room. Shaw and Root both turned and looked at Elizabeth, who continued.

"I'm here and ready to go. I'm not you, Root but I've got both of your backs- always."

Shaw smiled and Root relaxed back into her bed, defeated but somewhat relieved.


	7. Chapter 7

Harold was busy on his laptop. John approached Root's bed stone-faced. Shannon and Dr. Tillman looked at Elizabeth with concern and fear across their features. Dr. Tillman reached for Elizabeth's arm.

"Beth, don't do this. It could be dangerous. I couldn't bear…." The doctor's voice trailed off and she glanced at Shannon who was staring at her daughter.

"That's right honey. It's too dangerous… why don't you leave it to those guys, they are professionals."

Elizabeth's face reddened briefly, anger flashing in her eyes.

"Before your accident, _Mother,_ I was one of those professionals. If you hadn't needed me, I would have been doing this stuff and more for the last year or so.

"I know how to take care of myself, I know what I'm doing _and_ these are my friends as well as teammates. If they go into a situation and I stay back when I can help… well that ain't happening. Now this conversation is over- we have work to do."

She approached Finch, who was still working feverishly on his laptop. Shaw walked over to Dr. Tillman and Shannon. She smiled gently.

"Elizabeth is as good as any operative I worked with before I joined these guys. She has gotten out of situations that would have taken down some of the most capable people I worked with in ISA.

"Hell, she's a _badass._ I don't think I can pay her a higher compliment.

"I can't guarantee her safety anymore than you could guarantee that Root was going to be fine yesterday. But I can tell you that she's going into a situation she's trained for and is capable of handling, with competent people as her teammates and back-up.

"And knowing she's with me will give Root comfort, even though she'll be frustrated and worried."

Root smiled at Shaw's words and nodded.

Dr. Tillman and Shannon glanced at each other. Dr. Tillman was the first to crack.

"When you put it that way, Ms. Shaw, it's hard to argue."

Shannon looked at them and nodded reluctantly.

John, quietly fuming, took this opportunity to approach Finch.

"I'm in… and don't argue with me. I'm ready- and all the PT people agree with me."

Finch looked up from his laptop and called Dr. Tillman over.

"Why don't you and Ms. Ruben give us some time? We need to strategize and, quite frankly I don't want you getting concerned- sometimes these sessions get a little intense."

Dr. Tillman looked at John and shook her head.

"Fine- but Mr. Reese… oh never mind." She gently took Shannon's arm and led them from the room.

Once alone, Finch looked at the group.

"I wanted us alone but not because I was concerned with their reaction to our strategizing. It's our number."

Finch approached the bed and set his laptop on it so everyone could see it. The picture on screen was of an African-American man in his late teens to early twenties. He was handsome and looked vaguely familiar.

"His name is Carson West Jr. His father was just here an hour ago. I don't want either the doctor or Ms. Ruben tipping him to his son's situation until we have it in hand. We should be able to eliminate any threat to the young man without causing undue stress to Dr. West.

"If necessary, we can advise the doctor of his son's situation, but I would prefer to do it after the operation is complete and the threat eliminated."

Shaw looked at Finch.

"Do we know what the threat is?"

"Yes, and it's lethal, but we have time to intervene. A local gang leader has put out a hit on young Mr. West for interfering with his activities."

Another picture appeared on screen. A twenty-something man with shaved head, piercings and two tattoos on his face, one a tear drop, appeared.

"This is Julian Davis- JD to his friends, or maybe cronies would be a better word. He apparently came her from East St. Louis six months ago after being driven out by rival gang members. Once here, he tried to establish himself as a force in drug trafficking.

"He also dabbled in prostitution, and here's where he and young West clashed. Two weeks ago, one of Davis' women escaped the house she was being held in and sold to whomever. As she was about to be recaptured, West happened along in his car.

"He managed to get the woman to safety, however his identity was discovered by the thugs who were after the woman. Davis thinks he can make a name for himself in the area's underworld by eliminating West and securing his reputation as a man not to be crossed.

"I think Mr. Davis can be persuaded to set up his enterprises somewhere else if he believes there is a heavy mob presence in Albuquerque. The plan the Machine has devised may work without getting law enforcement involved which would be beneficial to us, to Dr. West and to his son- not to mention the women who are currently being held in the same warehouse the first one escaped from.

"Davis is a neo-Nazi and a pig, but exposing Dr. West to this could compromise his ability to be of assistance to us, not to mention our whole operation here at the hospital. Getting him to leave is a better alternative to getting the police involved.

Shaw frowned at Finch.

"Wouldn't killing him be a more efficient solution?"

"Probably, Ms. Shaw, however do we really want to start down that road, especially if we're trying to give the Machine a moral code of sorts?"

"Touche. Why do we 'have time' as you said?"

"The Machine has interfered with Davis' cash flow and he's been unable to produce the down payment on the hit. We have until tonight to implement the plan that will get Davis to leave without putting the hit in motion."

"So what's the plan?"

"It's fairly simple and straightforward. Mr. Reese, yes, you will be involved. John will be our 'Mob boss'. Ms. Shaw and Ms. Ruben will take Davis to Mr. Reese where he will intimidate Davis into leaving the area.

"Davis has a mother and two young siblings still living in East St. Louis. By all accounts, these are the only people he cares about. Mr. Reese can threaten to have them eliminated unless he gets out of town by tonight, and takes his small gang of thugs with him.

"Tell him you don't care where he goes as long as it's not here. Tell him you'd kill him but it's cleaner for him to just leave, maybe you don't have to spend so much covering up your activities by bribing local law enforcement.

"We may have to persuade Davis we're serious, but today we can restrict it to shooting kneecaps unless something unforeseen occurs. We also want to bring young Mr. West to a secure area before this all goes down. I thought Ms. Shaw and Mr. Reese could go pick him up and bring him here before you three go to meet Davis.

"That gives Ms. Ruben time to join the consult with Dr. West and Dr. Tillman this afternoon. Once Junior is safe and secure, you three are a go. I'm securing a private room in one of the hotels near the airport for the meet. Oh and John….."

Reese looked at Harold.

"You're still not 100 percent cleared. Please don't get too out of control."

"No worries, Finch. I promise to be restrained- as long as nothing unusual happens."

Harold raised his eyebrows.

"I'm sure."

….

Several hours later, with Dr. West's son safely at the hospital, Elizabeth and Shaw pulled up to a rundown apartment complex in a seedy part of Albuquerque. As they waited, Shaw looked over at Elizabeth and smiled.

"Just a heads up, Elizabeth- you and Dr. Tillman are doing a piss poor job of being discreet. It's probably not your fault- sometimes chemistry just wins. From what I've been told, everybody knew about Root and me before I would even admit there was a Root and me.

"I'm just letting you know I've seen your mom looking at the two of you like she knows, at least during her more lucid moments. And she's going to start having more and more lucid moments now that she's here. It's just a matter of time before they figure out a strategy to help her."

"I know we've been obvious Shaw. Hell, I don't know what to make of this whole situation. I was never a big 'relationship' person until I got involved with all of you. My relationships were all tied to a computer and lines of code. Maybe with only a mother who had her own life and absent a dad, I never learned about relationships.

"I figure if I concentrate on letting this 'thing' with Megan develop, the rest will sort itself out. But since I've never had something like this before, I'm learning as I go. Right now, I'm focused on Megan when we're together and not on hiding anything."

"That's probably the way it should be Elizabeth, but none of us are very good relationship people- just a group of loners who bonded over a cause."

"Maybe that's all _any_ of us are Shaw- loners who bond over different causes. Maybe those relationships are our causes."

"OK, Dr. Phil, I'd love to continue this but our target just showed."

Half a block ahead an older model Explorer pulled to the curb and three men exited. Davis climbed out of the back seat after the two in front had glance around in a pathetic sweep of the area. The group had to walk past Shaw and Elizabeth's vehicle, a newer minivan with markings indicating a flower shop, to get to their entrance.

As they passed, the two ladies followed. Shaw opened the rear hatch electronically, then the two quickly approached the group from behind. Shaw tased Davis then stepped back as he fell between his two "bodyguards". The two turned, gaping at their fallen leader, then before they could even react, went down holding their knees.

Shaw and Elizabeth dragged Davis to the back of the van, threw him in and jumped back in the front seats. As the two injured men writhed in pain on the sidewalk, the van pulled into the street and around a corner.

The entire operation took less than three minutes from the time Davis' crew first exited their vehicle. Shaw looked over and smiled.

"Nice job, Elizabeth."

Elizabeth smiled back.

"Thanks, let's get this asshole to John."

….

Davis' returned to awareness thinking he was dead. When he opened his eyes all he saw was pitch black. As he became more aware, he realized someone had put a hood over his head and secured him to a chair. His fear manifested itself in bravado, which lost a little of its bite since his voice was muffled by the hood.

"I'm going to kill you." The words came out muffled and weak and Davis realized it as he said them. "What do you want?" Got the hood removed.

As his eyes adjusted to being freed from the blackness, he realized he was sitting in front of a desk. The desk was in front of a large window which, because of the sun's position, blinded him to the figure sitting at said desk.

A voice came from the shadowy figure.

"You've gotten yourself into some trouble, Mr. Davis. I'm feeling generous today, so I am going to give you an opportunity to get yourself out."

Davis didn't recognize the voice. He looked down at his wrists and noticed they were zip-tied to the arms of the chair. He started to turn his head from side to side to see who and what was behind him when he felt a stinging pain in his right cheek.

"I wouldn't turn my head if I were you. That was just a scratch- the next time you'll be marked. You will be marked so ten years from now people will still flinch when they see you. If you still persist in turning your head, the second time you'll lose an eye. The third time you'll never be able to identify _anyone_ again.

"Do I make myself clear?"

A hand came into his field of vision. In that hand was a surgeon's scalpel. It was stained with enough blood to give credence to the threat. Suddenly the blade flashed downward, severing the tip of Davis' little finger of his right hand. As his head reared back uncontrollably, the hood was returned to his head and a hand covered his mouth, muffling his scream.

As agony marched up his right arm, a second searing sensation caused him to temporarily black out. Moments later, as the fog of pain began to lift, the hood was removed again. As Davis blinked the tears back and shook his head, the voice returned.

"Consider that your final warning, Mr. Davis. My colleagues and I don't have the time or the patience to play games with you. The only reason your body isn't in the dumpster behind your apartment building is that I pay good money to keep local law enforcement from interfering with my enterprises. With that goes a certain protocol- and leaving bodies behind is not part of it.

"Now in ten minutes I am going to leave this room. You will be given a sedative which will put you to sleep for less than an hour. When you awaken you will leave this room, leave this building, go back to your apartment and leave both this town and this state.

"If you do, I'll let you start over and irritate some other people in some other part of the country…"

The voice paused for a full thirty seconds.

"If you don't, the consequences will be serious."

A hand reached around with the scalpel- a warning to not move. Then the scalpel disappeared, only to be replaced by a picture- and Davis gasped.

"No, please not my family…. leave them alone…. oh God I'll go, I promise I'll go."

"Mr. Davis, this is not a game, you _will not_ receive any more warnings. Do you understand?"

"Yes, yes, God, please, I'll go…. I'll go tonight."

"You'll go immediately- if you don't I'll send you your baby sister's ear as a little reminder. Then, if you get anywhere near this town again, I'll send you the head that ear was attached to.

"We're done here."

….

Forty-five minutes later Elizabeth, John and Shaw arrived back at the hospital. Shaw disappeared into the rest room to finish cleaning up. John and Elizabeth waited, but when five minutes turned into ten and no Shaw, Elizabeth knocked on the door.

"Shaw?"

No answer.

"Shaw, are you OK in there?"

No answer. Elizabeth looked over at Reese, concern written on her face. John approached the door and banged on it.

"Shaw, Hey Shaw! Open the door."

When there was no answer, Reese reached into the inside pocket of his suit coat and removed a small lock picking kit. Thirty seconds later they heard a click and John opened the door. They could only get the door open a foot or so because something was blocking it. Elizabeth slipped through and looked toward the left.

"Shaw!"

She pulled Shaw's body away from the door so John could enter. Shaw had collapsed against both the door and the wall less than three feet behind the bathroom's sink. She showed no outward sign of injury but was unresponsive when Elizabeth tried to awaken her.

She looked at Reese.

"Get Megan- now!"

Reese nodded and left the bathroom.

Within five minutes Dr. Tillman and John were at the door. Dr. Tillman entered, checked Shaw's vitals and used her flashlight to check Shaw's eyes. She looked at Reese and Elizabeth, concern written on her face.

"We need to get her upstairs and we need to get Dr. West back here- stat."


	8. Chapter 8

Shaw became aware of voices, first off in the distance, then increasing in volume as if they were approaching. The darkness faded slowly into a gray fog, then began to brighten. She slowly opened her eyes and the glare of the examining room made her wince in pain. The simple act of shutting her eyes sent waves of pain and nausea cascading through her head. Her groans were quiet but Dr. Tillman was immediately at her side.

"Ms. Shaw, Sameen- Dr. West is on his way, he's asked me to prep you for a brain scan. We're not sure what caused your collapse but we're going to figure it out and make sure it gets addressed. Please stay as still as possible, we don't want any sudden movements to add to any issues."

Shaw did a quick inventory of her senses. Her head felt like someone was drilling for oil from the outside of her neck on the right side. There was some numbness in her hands and feet and a tingling sensation in her legs. _Classic stroke signs? Something worse?_ The doctor in her remained aloof from the patient's mild panic.

She raised her right hand and motioned Dr. Tillman over and waved her in close so she could whisper into the doctor's ear.

"Don't tell Root."

Tillman smiled and nodded.

"Don't worry Ms. Shaw. Everything's going to be alright."

Shaw sank back into darkness.

….

When Dr. West arrived, Shaw had been out for almost an hour after her brief return to consciousness. West examined her briefly, spoke to Elizabeth and John, and consulted with Dr. Tillman. Before the doctors took Shaw up to Imaging, Dr. Tillman spoke to the others about Shaw's request not to inform Root.

"Let's see what we find, then we'll make a determination."

As they wheeled Shaw toward the brain scan, Dr. Tillman remembered what occurred when Elizabeth and Shannon arrived.

"We were outside waiting for them to arrive when she suddenly had a stabbing pain in her head. When I mentioned it, she said she hadn't enough caffeine that day. I didn't really dwell on it because minutes later Elizabeth arrived with her mother."

West nodded.

"You couldn't have known. I have my suspicions but we need to do both a CT Scan and MRI so we have complete data on her condition. Then I want to interview all who've spent time with her during the past eighteen months or so."

Dr. Tillman frowned. "Ms… Root as well?"

"Yes of course. I know she doesn't want Ms. Groves to know, but if it comes down to needing information to treat her and protecting Ms. Groves' feelings, there's no contest."

….

The two doctors were looking at several screens of imaging and computer reports. Dr. West pointed to an area on one of the screens.

"See that point of light? That's the culprit in my opinion. Somehow, a small object has managed to work its way into Ms. Shaw's left temporal lobe. It's caused a subdural hematoma which you can see as the darker mass toward the rear. I'm fairly certain this is what caused both her pain episode, which you witnessed and her loss of consciousness today.

"I'd like to discuss with her friends if there have been any behavioral changes such as emotional outbursts, laughing or crying fits or any unusual behavioral episodes. The pressure could actually be building gradually in areas like the amygdala which controls some emotions.

"We need to remove the object, drain the excess blood from the temporal lobe and seal off the source of the blood leakage. It needs to be done immediately before either the hematoma itself causes permanent damage or ruptures completely and kills her.

"We can do it without invasive surgery, however if anything goes wrong we have to be prepared to open her skull and reduce any rapid increase in blood flow into the temporal lobe. We have to monitor her situation closely to avoid any brain damage. If we're fortunate, we can get in, get the object and stop any leakage without doing any permanent damage to Ms. Shaw's brain.

"One way or the other, we need to proceed quickly and eliminate the danger. I'm afraid she's been on borrowed time for quite awhile. Let's get going."

….

The operation should have been straightforward. An incision behind the right ear for access to the unidentified object, removal then suctioning of excess blood that was causing pressure inside the brain. Following removal of the object would be a short observation period to locate the exact source of the blood leakage.

Once the source of the leakage was located it should only take about fifteen minutes to repair and close.

That was ideally. Unfortunately, the object itself had become imbedded in the brain due to scar tissue which had grown around it. This slowed the doctors down considerably and added to the danger which the blood posed. The longer they waited the more pressure built.

At the moment of removal, after thirty minutes of painstaking work around the object, both doctors and nurses held their collective breath. Once actual removal occurred, the most dangerous part of the surgery presented itself.

There was a slight, yet significant possibility that the object was actually preventing blood from cascading into Shaw's brain, and removal would unleash a flood into the brain which could permanently damage her brain or kill her. There was an eerie silence in the operating room as Dr. West worked on the object.

It came free and the area held. Ten seconds passed, then twenty. After a full minute where no one in the room either moved or spoke, Dr. West looked up at the monitor and released a breath he didn't even realize he was holding.

"Looks like we're OK. Let's find the source of the leakage and get out of here."

Within the hour Shaw was being wheeled into recovery, where she would spend the rest of the night. It was two fifteen when they finished and both Drs. West and Tillman were exhausted. Smiling, they bid each other good night and went their separate ways.

Dr. Tillman headed for her office where she planned to spend the night. She had long ago moved a bed and some of her personal items into a room behind her office for nights like these. She was in the middle of brushing her teeth when her phone vibrated- a text.

The number was blocked.

 _See Root, tell her everything. Now._

She stared at the screen for almost a minute. Shaking her head at the insanity, she headed over to Root's room where she found the hacker sitting up in bed waiting for her.

"Talk to me doctor. She says you need to bring me up to speed on something. Where's Sameen? I haven't seen her since she went to work the number."

"She's fine…. at least she will be." Dr. Tillman went on to brief Root on the events of the last 12 hours and Shaw's prognosis.

"She should wake up sometime this morning and we can check her condition over the next 72 hours. The surgery went fine and it appears we have everything under control. The hematoma has been repaired and the offending object removed- we anticipate no complications.

"There is a question, of course, relating to any residual affects from both the leakage and the object that caused it. We will have to monitor her over the next few weeks to ensure there are no issues."

Root frowned.

"What was the object?"

"We're not sure, we sent it to pathology."

"I need to see it when they're done. Now tell me more about the procedure."

Something was nagging at Root's subconscious… why had the Machine insisted to both that they discuss this immediately? Sure it was serious, but the timing led Root to believe there was another issue at play that needed to be addressed.

As Dr. Tillman explained the procedure, Root periodically interrupted with questions. As they reached the discussion of the final clean up and close, Root's eyes flashed.

"Why didn't you open her skull? Brain surgery always seems to require it doesn't it?"

"In this case, Ms. Shaw's areas of concern were all in the lower rear of her brain cavity. We could access below her skull and work into the affected areas from entry gained behind both of her ears. This way…."

"That's _it_! That's why we're doing this now. Doctor, you have to get me into that recovery room. I need to be there when she wakes up. If not, she may very well find a way to kill herself before we can stop her."

"What are you talking about Ms. Groves…Root?"

"We've never talked with you about the _months_ Shaw spent in Samaritan's hands. They implanted a chip in her head which allowed them to run simulations. Those simulations were run with one goal in mind- getting Samaritan access to the Machine so it could be destroyed.

"They were very creative with the scenarios in their attempts to locate the Machine. During these simulations, Shaw killed lots of people, including John on more than one occasion. The one person she told me she couldn't kill was _me._

"Over and over again, _she killed herself to keep me safe._ If she thinks she's back in a simulation, she may very well try to kill herself as a way of keeping me safe and a way of resetting the simulation."

"Why would Ms. Shaw think she's back in a simulation?"

"After we got her back, we removed the chip from her head but periodically I would catch her checking that area behind her ear for the wound. If it appears to her there could be a chip back there, she may flash back to her captivity and could be a danger to herself.

"I can talk her down. I can reassure her this is real. I _need_ to be there when she wakes up.

"Please, Dr. Tillman, get me over to her."

It was the desperation in Root's eyes that convinced the doctor. She pulled out her phone and started giving orders. A wheelchair arrived ( _"You will not walk over there!"_ ) and they headed toward Recovery. By the time they arrived, the recovery area had been slightly altered to allow space for Root to sit next to Shaw's gurney while she awaited her regaining consciousness.

Dr. Tillman got Root situated and gave the nurses specific instructions to have someone with them all the time until Shaw awakened. She told Root she was sleeping in her office and would be available on five minutes notice if necessary.

Root thanked the doctor and began the vigil. As she sat beside Shaw's bed, she went over different possibilities she could use to convince Sameen that this wasn't a simulation. Everything she considered seemed to have holes that might leave Shaw unconvinced.

Then a light went on in her head. Root smiled.


	9. Chapter 9

Root sent a text to Dr. Tillman and Elizabeth.

 _I need to talk to the two of you._

Dr. Tillman's response was almost instant.

 _Is 20 minutes OK?_

 _Yes_

 _I'll be there._

Elizabeth's was somewhat slower. About five minutes after the doctor's text arrived-

 _You realize it's five AM right?_

 _Elizabeth- I assume you're not alone and you already know what's going on. I need to talk to both of you._

 _Fine_

Root smiled to herself as she went over her plan.

One floor down and a few corridors away, Elizabeth was dressing in the room behind Dr. Tillman's office.

"She can be so annoying at times. It's like she hacks people as easily as she hacks computers."

"I haven't known… Root as long as any of you but I know she's one of the smartest people I've ever met. I also know she loves Ms. Shaw with more…. I'm not sure the best word to describe it- enthusiasm, fervor whatever, than I may have ever witnessed.

"I'll say this, I've had few relationships and my career has always come first. If I'm ever in a relationship that's more than casual…"

At this, Megan paused and waited for Elizabeth to look over. When she did, she raised her eyebrows communicating without speaking.

".. and I feel that kind of love coming off him.. or her… I will grab onto them and never let go."

At this, Megan's cheeks flushed bright red.

Elizabeth hesitated briefly, then walked over and took both of Megan's hands in hers.

"I've never had any more than causal relationships either. I have a feeling about us that this might be different. I really don't have experience at this in any direction other than physical. I've got a past and I assume you do too. I'm not afraid of my past, and I'm not interested in yours.

"I wasn't necessarily ready to have this conversation, but I think I knew it was going to happen between us sooner rather than later… When I'm with you I feel like I'm headed into uncharted waters. I want us to be more than a casual fling… and I'm not sure how to proceed."

Megan smiled and tilted her head.

"Neither am I but maybe we should just keep going like we have been and see where it leads. As far as our pasts are concerned, I'm not afraid of either of ours, I'd like to concentrate more on discovering if we have a future."

Elizabeth smiled and brushed Megan's cheek with her lips. The doctor smiled faintly.

"We'll talk more- now we have to go."

….

When Dr. Tillman and Elizabeth arrived at the recovery area, they found Root's wheelchair next to Shaw's gurney and Root holding her hand. Sameen was still unconscious. Root looked up, smiled and indicated the two recliners she had requested.

"Please sit down. I'm afraid we have more than Sam's recovery from the surgery to worry about. Dr. Tillman, you and I spoke about my fears a few hours ago- Elizabeth, I want to bring you up to speed on Shaw's time with Samaritan and the fallout."

Root proceeded to go back to the Stock Exchange and explain everything that she had discovered about Sameen's abduction, torture and escape at the hands of Samaritan. As she recounted the story, a few tears managed to slip out of her eyes and slide down her cheeks. Both ladies were moved at the obvious emotion the retelling triggered in Root.

"Sam's default in these situations was to kill herself to avoid any possibility of hurting me. We've long since moved past the point where I worried about her flashing back to the captivity and the simulations. But with this particular trauma, I'm afraid she may start to worry this is _all_ a simulation.

"I've figured out a way we can convince Sam this is real and not a simulation, but I need to prep you and get your cooperation for this to work. And it may be uncomfortable- _for both of you._ "

Dr. Tillman spoke first.

"She's my patient now Root, as well as my friend. If you have a plan that can help her recovery and avoid any repercussions, I'm in."

Elizabeth only nodded.

"OK, when I explain everything, you'll see why we have to have this talk first. Both of you were part of Sam's life before Samaritan came on line, then you were gone, so its knowledge of you would have been sketchy at best.

"Sam know's this, but it is possible that there is some external knowledge of your relationship to the team. Therefore, your presence in a 'simulation' is not out of the question. Now, before I continue, I have to tell you I'm going to bring up some things that went on between you, Elizabeth, and Sameen before Sam and I were together."

Elizabeth reddened slightly and looked down at her lap. Megan smiled and reached over and took Elizabeth's hand.

"Funny you should bring that up, Root, we were just talking about this. I just got done telling Beth that I have no concerns about our pasts, just any possible future. So whatever you want to bring up is fine with me."

Elizabeth took a deep breath and let it out.

"I think I know where this is going, Root and I'll do whatever you need me to for her." She indicated Shaw, who by all indications was still under.

Root smiled and continued.

"I thought if we were all here when she wakes up, we can explain what's going on, then Dr. Tillman and I can leave you two alone. That will give you an opportunity to discuss some of the things that went on between you when you were alone at some of the safe houses."

Root stopped and gave both some time for her words to sink in, then continued.

"I know a little about those events but think coming from you it would convince Sam that this is real and no possible simulation. You see, what the safe houses had that few other areas did was absolute privacy. No one but those who were there could have known what went on.

"You would know details and entire events that Sam and I have never talked about. We really never discussed any of our pasts, except how they related to us and our relationship. I still don't have any desire to know any details of her past that might be uncomfortable for either of you to talk about.

"I guess if Dr. Tillman is interested or feels she should be around to observe while this is going on I can see that, but ideally just the two of you talking about events that only you two know about should be enough to convince her."

Dr. Tillman smiled again.

"I only have two concerns- Elizabeth and Shaw's safety. If Beth is OK with this, and we are certain Ms. Shaw won't be a danger to either, I am totally comfortable and don't need to be around. Elizabeth?"

"I'll be fine…" as the others looked at her, concerned, she continued… "no seriously, I'll be fine. I'm just thinking about some of the stuff we'll be talking about."

A voice came from the gurney.

"What's going on you guys, and why does my head feel like it's been run through a washing machine?"

Dr. Tillman popped out of her seat and headed for Shaw. After a brief examination, she began to explain.

"Ms. Shaw, you had a serious episode yesterday. Dr. West performed emergency surgery on you to fix bleeding in your brain. We believe everything went fine, but need to keep you here for a few days to a week to ensure you are in no more danger.

"I think I'll let.. Root tell you the rest."

Root turned the wheelchair back toward her love and reached out to take her hand.

"Sam, they had to go into your brain to fix a problem. While in there, they removed a small object that was causing your brain bleed. I think it was part of the chip Samaritan implanted back when they had you."

At this, Shaw's eyes widened and she reached for that place behind her ear. Root restrained her gently.

"Sam, you can't touch that area, it's one of the places Dr. West went in to fix what was wrong. And that's also why we're here. When I found out how they had to go in to fix this, I was afraid you'd react to the wound behind your ear as if this was a simulation.

"I won't take any chances with you being transported back to that time. As I said to you the night we reunited in the park, 'I can't live without you'. It's just as true now, maybe more so, as it was then.

"I asked Dr. Tillman and Elizabeth to be here when you woke up so we could convince you, if you had any doubts, that that this is real, and not any simulation."

Shaw looked at Root, doubt on her features.

"How do you think you can do that?" There was just a slight tremor in her voice indicating the fear she was feeling.

"Sam, you know that both Dr. Tillman and Elizabeth were before Samaritan became a threat. There's no plausible scenario that could put them in a simulation. However, on the off chance that their presence could have been a simulation, I want you and Elizabeth to talk about some of the details of what you two did when you were at some of the safe houses.

"As you know, nothing that went on in there would ever be known by anyone other than the two of you. Dr. Tillman and I are going to leave in a minute and leave you two so you'll be free to talk about anything and everything that went on.

"I know you're smart enough to realize that there's no way any simulation could have that information and you'll be assured this is real.

"Sam, I don't want you to be concerned in any way, I just want you to know this is real and we can begin to figure out how to get on with _both_ of our recoveries."

Shaw's eyes flashed what could have been hope and relief, but was quickly masked. She looked over at Dr. Tillman.

"How soon can we get this over with? I don't want to wait."

"Root and I are leaving now. We'll be back when Beth calls us on her phone."

Dr. Tillman took Root's wheelchair and led them to the door. Elizabeth slid the recliner over to Shaw's gurney, took her hand and smiled down. As the door slowly swung shut, they heard Elizabeth say,

"Maybe we should start by talking about how you got me over my fear of the dark."

….

Forty-five minutes had passed since they had left Shaw and Elizabeth alone. Root looked up at the clock, then at the doctor.

"Are you OK? I'm unconcerned about anything they're talking about, but you two are at the beginning of whatever is going on with you. I know as a doctor, you're fine with this- how about as a person?"

Dr. Tillman's eyes shot up and she shook her head. A smile appeared.

"I keep forgetting how smart and observant both you and Ms. Shaw are. When Beth and her mom showed up, Shaw looked at me and said I should relax- that Shannon would like and accept me. Now you and this situation.

"I'm fine. I told Beth I didn't care about her past and I don't. I only care about the future. My biggest concern is Ms. Shaw's overall health and recovery. Anything that aids in that process is fine with me. Really… Root, I'm OK. Sorry, but calling you that is going to take some time."

"It's ok, doc, I appreciate your effort."

Dr. Tillman's phone interrupted.

"Hi Beth, what's going on?"

She listened for a few seconds, then hung up.

"Let's go back."

….

When Dr. Tillman wheeled Root back into Shaw's recovery room, they found the two of them laughing and joking. Shaw looked over and smiled at the two.

"Hey, you're back. Thanks Root, I think you knew what you were doing. I was a little concerned, and would have freaked had I not been prepared for the marks from surgery. I knew I kept you around for a reason."

She smirked and Root smiled and winked. _Damn, why does that always get to me? She winks like an old man with gas._ Turning to Dr. Tillman the smirk turned into a genuine smile.

"Looks like I owe you one for me too, doc; it's not just my girlfriend you saved."

"You called me your girlfriend, Sam, and in public!"

"It's a little late for discretion Root, we live together."

"Yeah, but I know how you feel about PDA's. And public declarations."

"Whatever. Look, I think I can assure you I know this is no simulation. Elizabeth and I talked about some things that couldn't have been re-created by Samaritan- or anything or anyone else."

Both blushed briefly, then recovered.

Dr. Tillman smiled at Shaw, then yawned.

"Good, because all of us, except possibly you, Ms. Shaw, are way overdue for some sleep. We'll see you later today. Come on Beth."

"Wait, what about Root?"

"I'm staying Sam, I can sleep in the recliner. That way if you need _anything_ I'll be right here."

The inflection Root put into _"anything"_ caused Dr. Tillman to stop halfway to the door.

"Remember you two, no strenuous activity for awhile. doctor's orders."

Both Root and Shaw groaned as the door closed.


	10. Chapter 10

A week had passed. Both Root and Shaw were progressing nicely. While still confined to the hospital, both had given up riding in wheelchairs and, as a result, Dr. Tillman was ready to release them with a few restrictions.

"No running, fighting, rescuing or killing for the next four to six weeks for you, Ms. Shaw and six to eight weeks for you Root." The doctor was proud of how Root slipped naturally off her tongue after days of practice.

"You will both be in my office twice a week until you get completely cleared. Ms. Shaw, you'll be seeing Dr. West once a week until cleared and Root will be with me on a teleconference with Drs. Brady and Ryan once a week until cleared.

"Neither of you will work with your team on any numbers until given complete clearance by all doctors involved in your treatment and care. I need to repeat that- you will not, I repeat _NOT_ , work any numbers until you treatment is complete and you've been released. We all made the mistake of believing Root was ready to resume her normal activities before we did a complete review. And before we realized what normal is for her… for both of you.

"I'm in the uncomfortable position of telling both of you something I normally would never say to a patient- I can't lose either of you. You're way past patient status, passing friend and headed toward family. Harold, John- whom I'm currently in the process of clearing with both Drs. West and Ingram, and Elizabeth are all onboard with this.

"We don't want to disable your implants, but we will if you two don't agree to our restrictions. Then you'd lose access to the Machine for the foreseeable future. I know you don't want that Root and I suspect Ms. Shaw, you feel the same."

Root's face was a mixture of disappointment and pique.

"How come she gets off two weeks before I do? Not fair."

"First, fairness isn't how we make medical decisions. Second, her surgery was slightly less invasive than yours and her recovery slightly faster. Thirdly, I can even it up, _but_ it would involve extending Ms. Shaw's release to coincide with yours, not the other way around. If you want to try to explain how she's restricted just so you can feel better, be my guest."

Root's eyes fell to her lap as she refused to meet Shaw's glare.

"Never mind, doctor, I'll be a good girl."

"What about you, Ms. Shaw?"

"I don't like it, but I'm going to follow doctors' orders. Let's face it, how can I nag Root if I won't follow my own recovery? I'll behave, but I don't have to like behaving."

"You never liked behaving Sam." Root winked at her, and Shaw reacted as she always did to Root's attempts at winking.

"We will discuss some of this further." As both got up to leave Dr. Tillman's office, the doctor stopped them.

"Oh yes, and you can resume normal physical activities as far as everything outside of your work for the Machine goes."

She blushed slightly. Both Root and Shaw stared then, as realization set in, both smiled at each other.

"And Root could you stay just a minute longer. I have something else to talk to you about."

Shaw tilted her head, then shrugged.

"I'll be outside."

After the door closed, Dr. Tillman walked around to Root's chair. She stared at her briefly, then cleared her throat.

"You know…. Root…. I don't know if anyone's talked to you about this, but when you attempt to wink it resembles something almost… almost… well I don't know how to describe it but it's not normal. We have Physical Therapists that could help you with that."

"Normal, doctor, you mean like this?"

And Root winked- just like everyone winks. As Dr. Tillman stared, confusion on her face, Root smiled, then winked ( _normally_ ) again.

"I do it because it makes Sam crazy. I noticed it before I was shot- while everyone else snickered and made fun of it, for some reason it got to her. So one of the things I taught myself to do her after I woke up was wink like everyone else.

"But if I can make her _feel_ I want to do that because I think it helps her progress down that road toward feeling like the rest of us do. And I never cared what others thought, only Sam. So I still wink like someone with a deformity- for her."

"You never cease to amaze, Root. I'll see you later."

When Root walked out, Shaw looked at her.

"What was that all about?"

"Just gave me some ideas on how to make you crazy sweetie."

"Like you need any help in that area, _nerd_."

"Let's get Gen and head home. I'd like to start on some 'normal' physical activities- ASAP."

Shaw smirked.

"Me too."

….

Later that evening, Shaw and Root were relaxing in their room. The lights were off, the room only illuminated by two candles. Shaw had some music playing softly on her blue tooth speaker. As a piano played softly in the background and a raspy voice came through the speaker, Shaw turned and stared at Root.

Root, still recovering from 'normal physical activities' looked over.

"What is it Sam?"

"I've always thought of this as our song."

"Really? I like this, but I don't even know it's name, or for that matter, who's singing."

"It's 'Darlin Be Home Soon' by Joe Cocker. My parents danced to this at their wedding. My dad told me. He's a big reason I like some of the artists I like. He was constantly playing classic rock songs, and I suppose a shrink could make the case that I got into that genre to compensate for losing my dad so young.

"Anyway, the first verse started sticking in my mind when we were first past the 'I hate you and want to kill you' phase of our relationship.

 _"_ _Come,_

 _And talk of all the things we did today_

 _Here_

 _And laugh about our funny little ways_

 _While we have a few minutes to breathe_

 _Then I know that it's time you must leave_

 _But Darlin be home soon…_

"Because you were always running off around the world doing _her_ bidding, and I was obviously dealing with feelings I fought admitting to myself were real.

"Then, the Stock Market happened, Samaritan happened, and the night in the park happened… oh and of course you died. I had a hard time listening to this song after that, but then of course you came back to me… and all during that time, the second verse took on more meaning.

 _"_ _And now_

 _A quarter of my life is almost past_

 _I think I've come to see myself at last_

 _And I see that the time spent confused_

 _Was the time that I spent without you_

 _And I feel myself in bloom_

 _But Darlin be home soon….._

"Because you managed to take a sociopath and turn her into something resembling a feeling person. It never would have happened without you. Hell, Root, I hit the jackpot when this happened, I don't know how or why I got so lucky."

Root's eyes shimmered with unshed tears.

"I hope you realize that you're not the only one who feels like they got lucky. I never felt anyone could or should get into my heart after Hannah… of course who would have known I could meet someone like you- hot, dangerous and willing to put up with me.

"We are perfect for each other…. hey, would you play that song again…. and dance with me?"

"I thought you'd never ask."


End file.
